MAST - Motif Alignment and Search Tool
MAST version 3.0 (Release date: 2001/03/01 11:41:04)
For further information on how to interpret these results or to get
a copy of the MAST software please access http://meme.sdsc.edu.
REFERENCE
If you use this program in your research, please cite:
Timothy L. Bailey and Michael Gribskov,
"Combining evidence using p-values: application to sequence homology
searches", Bioinformatics, 14(48-54), 1998.
DATABASE AND MOTIFS
DATABASE farntrans5.s (peptide)
Last updated on Thu Mar 1 08:28:38 2001
Database contains 5 sequences, 1900 residues
MOTIFS meme.farntrans5.oops.4.sunsparcsolaris.html (peptide)
MOTIF WIDTH BEST POSSIBLE MATCH
----- ----- -------------------
1 32 QQPEGGFNGRPNKLPDVCYSWWVLGSLPIIGR
2 22 CQDEETGGFSDKPGNMVDFYHT
3 16 EAHAGYTFCATAALAI
PAIRWISE MOTIF CORRELATIONS:
MOTIF 1 2
----- ----- -----
2 0.46
3 0.47 0.18
No overly similar pairs (correlation > 0.60) found.
Random model letter frequencies (from non-redundant database):
A 0.073 C 0.018 D 0.052 E 0.062 F 0.040 G 0.069 H 0.022 I 0.056 K 0.058
L 0.092 M 0.023 N 0.046 P 0.051 Q 0.041 R 0.052 S 0.074 T 0.059 V 0.064
W 0.013 Y 0.033
SECTION I: HIGH-SCORING SEQUENCES
- Each of the following 5 sequences has E-value less than 10.
- The E-value of a sequence is the expected number of sequences
in a random database of the same size that would match the motifs as
well as the sequence does and is equal to the combined p-value of the
sequence times the number of sequences in the database.
- The combined p-value of a sequence measures the strength of the
match of the sequence to all the motifs and is calculated by
- finding the score of the single best match of each motif
to the sequence (best matches may overlap),
- calculating the sequence p-value of each score,
- forming the product of the p-values,
- taking the p-value of the product.
- The sequence p-value of a score is defined as the
probability of a random sequence of the same length containing
some match with as good or better a score.
- The score for the match of a position in a sequence to a motif
is computed by by summing the appropriate entry from each column of
the position-dependent scoring matrix that represents the motif.
- Sequences shorter than one or more of the motifs are skipped.
- The table is sorted by increasing E-value.
| Links | Sequence Name | Description | E-value | Length
|
|---|
|
| RATRABGERB
| Rat rab geranylgeranyl tr...
| 2e-59
| 331
|
|
| BET2_YEAST
| YPT1/SEC4 PROTEINS GERANY...
| 1.2e-56
| 325
|
|
| RAM1_YEAST
| PROTEIN FARNESYLTRANSFERA...
| 1.3e-53
| 431
|
|
| PFTB_RAT
| PROTEIN FARNESYLTRANSFERA...
| 2.3e-52
| 437
|
|
| CAL1_YEAST
| RAS PROTEINS GERANYLGERAN...
| 2.8e-42
| 376
|
SECTION II: MOTIF DIAGRAMS
- The ordering and spacing of all non-overlapping motif occurrences
are shown for each high-scoring sequence listed in Section I.
- A motif occurrence is defined as a position in the sequence whose
match to the motif has POSITION p-value less than 0.0001.
- The POSITION p-value of a match is the probability of
a single random subsequence of the length of the motif
scoring at least as well as the observed match.
- For each sequence, all motif occurrences are shown unless there
are overlaps. In that case, a motif occurrence is shown only if its
p-value is less than the product of the p-values of the other
(lower-numbered) motif occurrences that it overlaps.
- The table also shows the E-value of each sequence.
- Spacers and motif occurences are indicated by
- occurrence of motif `n' with p-value less than 0.0001.
- Sequences longer than 1000 are not shown to scale and are indicated by thicker lines.
| Links | Name | Expect |    Motifs
|
|---|
|
| RATRABGERB
| 2e-59
|
|
|
| BET2_YEAST
| 1.2e-56
|
|
|
| RAM1_YEAST
| 1.3e-53
|
|
|
| PFTB_RAT
| 2.3e-52
|
|
|
| CAL1_YEAST
| 2.8e-42
|
|
| SCALE
|
| |
| |
| |
| |
| |
| |
| |
| |
| |
| |
| |
| |
| |
| |
| |
| |
| |
| |
| 1
| 25
| 50
| 75
| 100
| 125
| 150
| 175
| 200
| 225
| 250
| 275
| 300
| 325
| 350
| 375
| 400
| 425
| |
|
|---|
SECTION III: ANNOTATED SEQUENCES
- The positions and p-values of the non-overlapping motif occurrences
are shown above the actual sequence for each of the high-scoring
sequences from Section I.
- A motif occurrence is defined as a position in the sequence whose
match to the motif has POSITION p-value less than 0.0001 as
defined in Section II.
- For each sequence, the first line specifies the name of the sequence.
- The second (and possibly more) lines give a description of the
sequence.
- Following the description line(s) is a line giving the length,
combined p-value, and E-value of the sequence as defined in Section I.
- The next line reproduces the motif diagram from Section II.
- The entire sequence is printed on the following lines.
- Motif occurrences are indicated directly above their positions in the
sequence on lines showing
- the motif number of the occurrence,
- the position p-value of the occurrence,
- the best possible match to the motif, and
- columns whose match to the motif has a positive score (indicated
by a plus sign).
RATRABGERB
Rat rab geranylgeranyl transferase beta-subunit
LENGTH = 331 COMBINED P-VALUE = 4.02e-60 E-VALUE = 2e-59
DIAGRAM: 126-[1]-29-[3]-19-[1]-15-[2]-40
[1]
2.1e-09
QQPEGGFNGRPNKLPDVCYSWWVL
+++++ + + ++ ++
76 KSCQHECGGVSASIGHDPHLLYTLSAVQILTLYDSIHVINVDKVVAYVQSLQKEDGSFAGDIWGEIDTRFSFCAV
[3] [1]
4.8e-16 7.6
GSLPIIGR EAHAGYTFCATAALAI QQP
++++++++ ++++++++++++++++ +++
151 ATLALLGKLDAINVEKAIEFVLSCMNFDGGFGCRPGSESHAGQIYCCTGFLAITSQLHQVNSDLLGWWLCERQLP
[2]
e-33 3.5e-24
EGGFNGRPNKLPDVCYSWWVLGSLPIIGR CQDEETGGFSDKPGNMVDFYHT
+++++++++++++++++++++++++++++ ++++++++++++++++++++++
226 SGGLNGRPEKLPDVCYSWWVLASLKIIGRLHWIDREKLRSFILACQDEETGGFADRPGDMVDPFHTLFGIAGLSL
BET2_YEAST
YPT1/SEC4 PROTEINS GERANYLGERANYLTRANSFERASE BETA SUBUNIT (EC 2.
LENGTH = 325 COMBINED P-VALUE = 2.34e-57 E-VALUE = 1.2e-56
DIAGRAM: 66-[2]-31-[1]-29-[3]-22-[1]-15-[2]-38
[2]
1.9e-05
CQDEETGGF
+ + + + +
1 MSGSLTLLKEKHIRYIESLDTNKHNFEYWLTEHLRLNGIYWGLTALCVLDSPETFVKEEVISFVLSCWDDKYGAF
[1]
4.3e-09
SDKPGNMVDFYHT QQPEGGFNGRPNKLPDVCYSWWVLGSLPIIG
+ + ++ + + +++++ +++ +++ + ++ + +++
76 APFPRHDAHLLTTLSAVQILATYDALDVLGKDRKVRLISFIRGNQLEDGSFQGDRFGEVDTRFVYTALSALSILG
[3] [1]
4.0e-14 3.5e-34
R EAHAGYTFCATAALAI QQPEGGF
++++++++ +++++++ +++++++
151 ELTSEVVDPAVDFVLKCYNFDGGFGLCPNAESHAAQAFTCLGALAIANKLDMLSDDQLEEIGWWLCERQLPEGGL
[2]
6.0e-22
NGRPNKLPDVCYSWWVLGSLPIIGR CQDEETGGFSDKPGNMVDFYHT
+++++++++++++++++++++++++ ++++++++++++++++++++++
226 NGRPSKLPDVCYSWWVLSSLAIIGRLDWINYEKLTEFILKCQDEKKGGISDRPENEVDVFHTVFGVAGLSLMGYD
RAM1_YEAST
PROTEIN FARNESYLTRANSFERASE BETA SUBUNIT (EC 2.5.1.-) (CAAX FARN
LENGTH = 431 COMBINED P-VALUE = 2.66e-54 E-VALUE = 1.3e-53
DIAGRAM: 153-[3]-37-[3]-33-[3]-20-[1]-19-[2]-67
[3] [3]
2.9e-05 7.1e-05
EAHAGYTFCATAALAI EAHAGYTFCATAALAI
++ + ++ + ++ + + ++++++ +
151 PGQLSHLASTYAAINALSLCDNIDGCWDRIDRKGIYQWLISLKEPNGGFKTCLEVGEVDTRGIYCALSIATLLNI
[3] [1]
9.0e-19 2.8e-27
EAHAGYTFCATAALAI QQPEGGFNG
++++++++++++++++ ++++++++
226 LTEELTEGVLNYLKNCQNYEGGFGSCPHVDEAHGGYTFCATASLAILRSMDQINVEKLLEWSSARQLQEERGFCG
[2]
1.7e-21
RPNKLPDVCYSWWVLGSLPIIGR CQDEETGGFSDKPGNMVDFYHT
++++++++++++++++++++++ ++++++++++++++++++++++
301 RSNKLVDGCYSFWVGGSAAILEAFGYGQCFNKHALRDYILYCCQEKEQPGLRDKPGAHSDFYHTNYCLLGLAVAE
PFTB_RAT
PROTEIN FARNESYLTRANSFERASE BETA SUBUNIT (EC 2.5.1.-) (CAAX FARNES
LENGTH = 437 COMBINED P-VALUE = 4.62e-53 E-VALUE = 2.3e-52
DIAGRAM: 133-[1]-19-[1]-29-[3]-20-[1]-28-[2]-74
[1]
5.4e-09
QQPEGGFNGRPNKLPDV
+++++++ + + +
76 EKHFHYLKRGLRQLTDAYECLDASRPWLCYWILHSLELLDEPIPQIVATDVCQFLELCQSPDGGFGGGPGQYPHL
[1]
5.8e-05
CYSWWVLGSLPIIGR QQPEGGFNGRPNKLPDVCYSWWVLGSLPIIGR
++ + + +++ ++++ + +++ ++ ++ + + +
151 APTYAAVNALCIIGTEEAYNVINREKLLQYLYSLKQPDGSFLMHVGGEVDVRSAYCAASVASLTNIITPDLFEGT
[3] [1]
2.0e-17 1.9e-29
EAHAGYTFCATAALAI QQPEGGFNGRPNKLPDVCY
++++++++++++++++ +++++++++++++++++++
226 AEWIARCQNWEGGIGGVPGMEAHGGYTFCGLAALVILKKERSLNLKSLLQWVTSRQMRFEGGFQGRCNKLVDGCY
[2]
2.0e-19
SWWVLGSLPIIGR CQDEETGGFSDKPGNMVDFYHT
++++++ ++++++ + +++++++ ++++++++++++
301 SFWQAGLLPLLHRALHAQGDPALSMSHWMFHQQALQEYILMCCQCPAGGLLDKPGKSRDFYHTCYCLSGLSIAQH
CAL1_YEAST
RAS PROTEINS GERANYLGERANYLTRANSFERASE (EC 2.5.1.-) (PROTEIN GER
LENGTH = 376 COMBINED P-VALUE = 5.69e-43 E-VALUE = 2.8e-42
DIAGRAM: 213-[3]-41-[1]-18-[2]-34
[3]
2.7e-14
EAHAGYTFCATA
+++++++ ++++
151 DYKTNCGSSVDSDDLRFCYIAVAILYICGCRSKEDFDEYIDTEKLLGYIMSQQCYNGAFGAHNEPHSGYTSCALS
[1]
2.8e-27
ALAI QQPEGGFNGRPNKLPDVCYSWWVLGSLPII
++++ ++++++++++++++++++++++++++++++
226 TLALLSSLEKLSDKFKEDTITWLLHRQVSSHGCMKFESELNASYDQSDDGGFQGRENKFADTCYAFWCLNSLHLL
[2]
3.0e-14
GR CQDEETGGFSDKPGNMVDFYHT
++ +++ +++++ +++++++++++
301 TKDWKMLCQTELVTNYLLDRTQKTLTGGFSKNDEEDADLYHSCLGSAALALIEGKFNGELCIPQEIFNDFSKRCC
Debugging Information
CPU: nbcr2
Time 0.340000 secs.
mast meme.farntrans5.oops.4.sunsparcsolaris.html -stdout
Button Help
Links to Entrez database at NCBI
Links to sequence scores (section I)
Links to motif diagrams (section II)
Links to sequence/motif annotated alignments (section III)
This information